Detection of Saint Louis encephalitis virus in two Brazilian states.

We describe the circulation of Saint Louis encephalitis virus (SLEV) in two Brazilian States during outbreaks of Dengue and Zika viruses. We detected the virus in a patient from Araraquara, State of São Paulo, and in patients and in a mosquito pool of Culex quinquefasciatus from Sinop, State of Mato Grosso. Phylogenetic analysis grouped samples from this study within genotype V, which are closely related to other strains that previously circulated in other parts of the country. Genotype V seems to have established circulation in Brazil.

COVID-19 Patterns in Araraquara, Brazil: A Multimodal Analysis.

The epidemiology of COVID-19 presented major shifts during the pandemic period. Factors such as the most common symptoms and severity of infection, the circulation of different variants, the preparedness of health services, and control efforts based on pharmaceutical and non-pharmaceutical interventions played important roles in the disease incidence. The constant evolution and changes require the continuous mapping and assessing of epidemiological features based on time-series forecasting. Nonetheless, it is necessary to identify the events, patterns, and actions that were potential factors that affected daily COVID-19 cases. In this work, we analyzed several databases, including information on social mobility, epidemiological reports, and mass population testing, to identify patterns of reported cases and events that may indicate changes in COVID-19 behavior in the city of Araraquara, Brazil. In our analysis, we used a mathematical approach with the fast Fourier transform (FFT) to map possible events and machine learning model approaches such as Seasonal Auto-regressive Integrated Moving Average (ARIMA) and neural networks (NNs) for data interpretation and temporal prospecting. Our results showed a root-mean-square error (RMSE) of about 5 (more precisely, a 4.55 error over 71 cases for 20 March 2021 and a 5.57 error over 106 cases for 3 June 2021). These results demonstrated that FFT is a useful tool for supporting the development of the best prevention and control measures for COVID-19.

A tale of 141 municipalities: the spatial distribution of dengue in Mato Grosso, Brazil.

BACKGROUND: In recent years, the state of Mato Grosso has presented one of the highest dengue incidence rates in Brazil. The meeting of the Amazon, Cerrado and Pantanal biomes results in a large variation of rainfall and temperature across different regions of the state. In addition, Mato Grosso has been undergoing intense urban growth since the 1970s, mainly due to the colonization of the Mid-North and North regions. We analyzed factors involved in dengue incidence in Mato Grosso from 2008 to 2019. METHODS: The Moran Global Index was used to assess spatial autocorrelation of dengue incidence using explanatory variables such as temperature, precipitation, deforestation, population density and municipal development index. Areas at risk of dengue were grouped by the Local Moran Indicator. RESULTS: We noticed that areas at risk of dengue expanded from the Mid-North region to the North; the same pattern occurred from the Southeast to the Northeast; the South region remained at low-risk levels. The increase in incidence was influenced by precipitation, deforestation and the municipal development index. CONCLUSIONS: The identification of risk areas for dengue in space and time enables public health authorities to focus their control and prevention efforts, reducing infestation and the potential impact of dengue in the human population.

First identification of Culex flavivirus (Flaviviridae) in Brazil.

INTRODUCTION: Culex flavivirus (CxFV) was first isolated in 2007 from Culex pipiens in Japan and then identified in several other countries. Characterization of the CxFV showed that all strains are related to the cell fusing agent virus. In this manuscript we report the first identification of CxFV in South America. MATERIAL AND METHODS: We have collected Culex sp. mosquitoes using BG-Sentinel traps and manual aspirators. They were pooled according to genus, species, sex and location. Viral RNA was extracted and multiplex nested PCR was performed to test the presence of Flavivirus. The positive samples were isolated in C6/36 cells and sequenced for phylogenetic analyses. RESULTS: 265 female Culex mosquitoes pooled in 83 pools were tested with specific CxFV, Saint Louis encephalitis virus (SLEV) and West Nile virus (WNV) primers. Our sequence data indicated maximum sequence similarity of 97% with CxFV. DISCUSSION: In this study we report the circulation of CxFV in an urban setting where SLEV had previously caused an outbreak. In terms of public health, this is an important finding due to the assumption that the previous exposition of mosquitoes to CxFV might lessen the susceptibility of these mosquitoes to other flaviviruses.

Population dynamics of DENV-1 genotype V in Brazil is characterized by co-circulation and strain/lineage replacement.

Following successive outbreaks of dengue fever caused predominantly by dengue virus (DENV) 2 and 3, DENV-1 is now the primary serotype circulating in Brazil. We sequenced and analyzed Brazilian DENV-1 genomes and found that all isolates belong to genotype V and are subdivided into three lineages, which were introduced during four different events. The first introduction occurred in 1984-85, the second in 1997-99, and the third and fourth occurred from 2004 to 2007. These events were associated with an increase in genetic diversity but not with positive selection. Moreover, a potential new recombinant strain derived from two distinct lineages was detected. We demonstrate that the dynamics of DENV-1 in Brazil is characterized by introduction, movement, local evolution, and lineage replacement. This study strengthens the relevance of genotype surveillance in order to identify, trace, and control virus populations circulating in Brazil and Latin America.

Serological detection of West Nile virus in horses and chicken from Pantanal, Brazil.

In an effort to detect West Nile virus (WNV) in Brazil, we sampled serum from horses and chickens from the Pantanal region of the state of Mato Grosso and tested for flavivirus-reactive antibodies by blocking ELISA. The positive samples were further confirmed for serological evidence of WNV infection in three (8%) of the 38 horses and one (3.2%) of the 31 chickens using an 80% plaque-reduction neutralisation test (PRNT80). These results provide evidence of the circulation of WNV in chickens and horses in Pantanal.

National Holidays and Social Mobility Behaviors: Alternatives for Forecasting COVID-19 Deaths in Brazil.

In this paper, we investigate the influence of holidays and community mobility on the transmission rate and death count of COVID-19 in Brazil. We identify national holidays and hallmark holidays to assess their effect on disease reports of confirmed cases and deaths. First, we use a one-variate model with the number of infected people as input data to forecast the number of deaths. This simple model is compared with a more robust deep learning multi-variate model that uses mobility and transmission rates (R0, Re) from a SEIRD model as input data. A principal components model of community mobility, generated by the principal component analysis (PCA) method, is added to improve the input features for the multi-variate model. The deep learning model architecture is an LSTM stacked layer combined with a dense layer to regress daily deaths caused by COVID-19. The multi-variate model incremented with engineered input features can enhance the forecast performance by up to 18.99% compared to the standard one-variate data-driven model.

Serological point-of-care and label-free capacitive diagnosis of dengue virus infection.

Dengue non-structural protein 1 (NS1 DENV) is considered a biomarker for dengue fever in an early stage. A sensitive and rapid assay for distinguishing positive from negative dengue infection samples is imperative for epidemic control and public health in tropical regions because it enables the development of instantaneous updatable databases and effective surveillance systems. Presently, we successfully report, for the first time, the use of the electrochemical capacitive method for the detection of NS1 DENV biomarker in human serum samples. By using a ferrocene-tagged peptide modified surface containing anti-NS1 as the receptor, it was possible to differentiate positive from negative samples with a p < 0.01 in a reagentless and label-free capacitive format. This capacitive assay had a cut-off of 1.36% (confidence interval of 99.99%); it therefore opens new avenues for developing miniature label-free electrochemical devices for infectious diseases.

Detection of the Asian II genotype of dengue virus serotype 2 in humans and mosquitoes in Brazil.

INTRODUCTION: DENV-2 is the cause of most dengue epidemics worldwide and is associated with severe cases. METHODS: We investigated arboviruses in 164 serum samples collected from patients presenting with clinical symptoms of dengue fever and 152 mosquito pools. RESULTS: We detected the Asian II genotype of DENV-2 in humans and mosquitoes. Our results confirmed the circulation of the Asian II genotype in Brazil, in addition to the prevalent Asian/American genotype. CONCLUSIONS: The detection of Asian II genotype of DENV-2 in mosquito pools collected in a forest park may be related to a spillback event of human dengue virus.

Ecological aspects of potential arbovirus vectors (Diptera: Culicidae) in an urban landscape of Southern Amazon, Brazil.

Amazon has been under intense human pressure, especially in the so-called "Arc of Deforestation" in the Eastern and Southern regions. Changes in biodiversity due to landscape disturbance in municipalities at the Arc of Deforestation are likely to impact mosquito species leading to the potential for emergence of arboviruses. Our aim was to describe the composition and structure of culicids in Sinop, a municipality located in the Southern Amazon at the State of Mato Grosso, as well as their presence in urban habitats, analyzing climate variables and potential risk of arbovirus transmission. Mosquitoes were collected in four habitats located in urban environments for 12 months. We recovered 5,210 adult mosquitoes from mosquito traps. Among the 33 species identified, 19 are associated with arbovirus transmission. Higher abundance, richness, diversity, and equitability of mosquito species were observed in urban forest parks and in new neighborhoods located in the outskirts of the city, nearby forest fragments and agricultural areas. As the environment consolidates as urban, both abundance and richness decrease. Highly urbanized neighborhoods had higher dominance of Culex quinquefasciatus, a mosquito associated with different arboviruses, including West Nile and Saint Louis encephalitis virus. The medically important species Cx. declarator, Cx. (Melanoconion) ssp., Aedeomyia squamipennis and Aedes scapularis were found in the four habitats. It is possible that these mosquitoes are adapting to different habitats and as a consequence, they are reaching urbanized areas. Mosquito abundance was higher in the days of high temperature and low precipitation in urban forest parks and in highly urbanized neighborhoods. These results suggest that Sinop region is a key area for surveillance of arbovirus vectors.

Spatial correlation of incidence of dengue with socioeconomic, demographic and environmental variables in a Brazilian city.

Dengue is endemic in most tropical countries. The reasons for its maintenance are related to several risk factors including socioeconomic factors. Urban space and time are also two important dimensions to describe the dynamics of an outbreak. The aim of this study was to evaluate the existence of a spatial correlation of the incidence of dengue and to identify variables that explain the spatial dependence in a medium-sized city of Brazil. We analyzed registered autochthonous dengue cases from September 1994 to August 2002 correlating them with socioeconomic, demographic and environmental variables using the Moran index. Our results indicate spatial dependence of the incidence of dengue and that socioeconomic factors were critical both at the beginning of the study and later on; other variables related to the organization of urban space were also involved in the occurrence of the disease. The use of spatial analysis tools is important to identify critical control areas with several variables intimately related to the modulation of the disease dynamics.

Assessment of entomological indicators of Aedes aegypti (L.) from adult and egg collections in São Paulo, Brazil.

We compared the presence and mean number of eggs from oviposition traps with the mean number of Aedes aegypti females captured by manual aspirators and by MosquiTRAPs to determine the sensitivity of each method and to standardize each indicator. The collections of adults and eggs were performed over 23 weeks in six neighborhoods of Mirassol, state of São Paulo, Brazil. A better assessment of indicators required larger number of MosquiTRAPs, but to quantify the number of females per house, one trap was sufficient. The sensitivities of MosquiTRAPs and manual aspirations to detect the presence of A. aegypti females were similar, but were lower compared to oviposition traps. The correlation coefficients between the number of females captured by MosquiTRAPs and manual aspirations and the number of eggs from oviposition traps were low, which may be a consequence of each method showing different stages of the mosquito life cycle.

Dengue in Araraquara, state of São Paulo: epidemiology, climate and Aedes aegypti infestation.

OBJECTIVE To describe the epidemiology of dengue in a medium-sized city in the state of São Paulo. METHODS Data, such as circulating serotypes, severe cases and deaths, age group, sex, among others, were obtained on reported and confirmed dengue cases in Araraquara, state of São Paulo, between 1991 and 2015. Climatic and infestation data were also analyzed. These variables were evaluated descriptively, using statistical measures such as frequencies, averages, minimum and maximum. Dengue incidence rates were calculated according to month, year, age and sex, and time series of dengue cases, infestation, and climatic variables. RESULTS Approximately 16,500 cases of dengue fever were reported between 1991 and 2015. The highest number of reports was recorded in 2015 (7,811 cases). In general, the age group with the highest number of reports is between 20 and 59 years old. The highest incidences, generally between March and May, occurred after the increase in rainfall and infestation in January. CONCLUSIONS Increased levels of infestation due to rainfall are reflected in incidence rates of the disease. It is fundamental to know the epidemiology of dengue in medium-sized cities. Such information can be extended to diseases such as Zika and Chikungunya, which are transmitted by the same vector and were reported in the city. The intensification of surveillance efforts in periods before epidemics could be a strategy to be considered to control the viral spread.

Using adult Aedes aegypti females to predict areas at risk for dengue transmission: A spatial case-control study.

INTRODUCTION: Traditional indices for measuring dengue fever risk in a given area are based on the immature forms of the vector (larvae and pupae surveys). However, this is inefficient because only adult female mosquitoes actually transmit the virus. Based on these assumptions, our objective was to evaluate the association between an entomological index obtained from adult mosquito traps and the occurrence of dengue in a hyperendemic area. Additionally, we compared its cost to that of the Breteau Index (BI). MATERIAL AND METHODS: We performed this study in São José do Rio Preto, SP, Brazil, between the epidemiological weeks of 36/2012 and 19/2013. BG-Sentinel and BG-Mosquitito traps were installed to capture adult mosquitoes. Positive and negative cases of dengue fever were computed and geocoded. We generated biweekly thematic maps of the entomological index, generated by calculating the number of adult Aedes aegypti females (NAF) per 100 households during a week by kriging, and based on the number of mosquitoes captured. The relation between the occurrence of dengue fever and the NAF was tested using a spatial case-control design and a generalized additive model and was controlled by the coordinates of the positive and negative cases of dengue fever. RESULTS: Our analyses showed that increases in dengue fever cases occurred in parallel with increases in the number of Ae. aegypti females. The entomological index produced in our study correlates positively with the incidence of dengue, particularly during intervals when vector control measures were applied less intensively. The operational costs of our index were lower than those of the BI: NAF used 71.5% less human resources necessary to measure the BI. CONCLUSIONS: Spatial analysis techniques and the number of adult Ae. aegypti females were used to produce an indicator of dengue risk. The index can be applied at various levels of spatial aggregation for an entire study area, as well as for sub-areas, such as city blocks. Even though the index is adequate to predict dengue risk, it should be tested and validated in various scenarios before routine use.

Field-deployable viral diagnostics using CRISPR-Cas13.

Mitigating global infectious disease requires diagnostic tools that are sensitive, specific, and rapidly field deployable. In this study, we demonstrate that the Cas13-based SHERLOCK (specific high-sensitivity enzymatic reporter unlocking) platform can detect Zika virus (ZIKV) and dengue virus (DENV) in patient samples at concentrations as low as 1 copy per microliter. We developed HUDSON (heating unextracted diagnostic samples to obliterate nucleases), a protocol that pairs with SHERLOCK for viral detection directly from bodily fluids, enabling instrument-free DENV detection directly from patient samples in <2 hours. We further demonstrate that SHERLOCK can distinguish the four DENV serotypes, as well as region-specific strains of ZIKV from the 2015-2016 pandemic. Finally, we report the rapid (<1 week) design and testing of instrument-free assays to detect clinically relevant viral single-nucleotide polymorphisms.

[Dengue Control Program in São José do Rio Preto, São Paulo State, Brazil: problems with health agents' work and population adherence]. / O Programa de Controle do Dengue em São José do Rio Preto, São Paulo, Brasil: dificuldades para a atuação dos agentes e adesão da população.

This study aimed to identify the aspects that interfere with the performance of vector control agents and community health workers and population adherence to dengue control programs. The focal group methodology was applied to discuss the relations between the program, health agents, and population. According to the results, dengue control and prevention were considered relatively unimportant activities, i.e., ideal community health workers would be capable of solving other (supposedly more important) problems. Vector control agents emphasized the population's lack of adherence and the fact that they (the control agents) were confused with garbage collectors (considered less important than community health workers, and with a focus more on productivity than quality). Women frequently blamed neighbors for the dengue problem and associated the disease with lack of hygiene. These aspects have a negative impact on dengue control agents' work and result from the program's vertical structure. Possible solutions would be to incorporate the agents into community health clinics, encourage cooperation between departments, and provide the conditions for them to intervene in the environment.

[Socioeconomic variables and dengue transmission]. / Variáveis socioeconômicas e a transmissão de dengue.

OBJECTIVE: To evaluate the relationship between risk of occurrence of dengue and socioeconomic level. METHODS: All confirmed autochthonous cases of dengue between September 1990 and August 2002 were geocoded and grouped according to the urban census tracts of the municipality of São José do Rio Preto, Southeastern Brazil. A socioeconomic factor generated by principal component analysis was used to group census tracts into four socioeconomic levels. Incidence rates were calculated for each year and four-year period for each of the census sectors, considering the period from September of one year to August of the next. Thematic maps of sectors, grouped into each of the four socioeconomic levels and their respective disease incidences, are presented. RESULTS: Principal component analysis generated a socioeconomic factor that accounted for 87% of total variation. This factor was associated with dengue incidence only for the 1994-95 period. CONCLUSIONS: The lack of an association between risk of occurrence of dengue and socioeconomic levels in almost all years studied indicates that this issue deserves further study, and may vary depending on the settings found in each municipality. It will be important to determine the spatial relationship between dengue transmission and other variables, such as degree of immunity in the population, effectiveness of control measures, degree of infestation by the vector; and population habits and behaviors, among others.

Physiological state of Aedes (Stegomyia) aegypti mosquitoes captured with MosquiTRAPs in Mirassol, São Paulo, Brazil.

We examined the best location in a house to install MosquiTRAPs, sticky ovitraps that attract and capture Aedes aegypti females and investigated the physiological state of captured female mosquitoes. The study was performed in a twenty-block area in Mirassol, São Paulo State, Brazil, in which five blocks were randomly chosen for MosquiTRAP installation. In each block, four houses were selected for the installation of eight traps: four indoors (bedroom, living room, bathroom, and kitchen) and four outdoors in the shade (two at the front of the house and two in the backyard). These houses were visited over an eight-week period. The outdoor MosquiTRAPs captured five times more females than indoor traps and appeared to be the best places to install MosquiTRAPs. There were no significant differences among indoor sites or among outdoor sites with respect to the number of females captured. The capacity of the MosquiTRAP to capture a large number of gravid Ae. aegypti females reinforces its potential as an entomological surveillance tool in dengue control programs.

[Dengue control in an urban area of Brazil: impact of the Family Health Program on traditional control]. / Controle do dengue em uma área urbana do Brasil: avaliação do impacto do Programa Saúde da Família com relação ao programa tradicional de controle.

A study was performed in different areas of São José do Rio Preto which include the Family Health Program (FHP) and the Dengue Control Program, and the results of integration between the two programs were evaluated. In addition to other responsibilities, community health agents instructed residents on dengue control measures, encouraging the population to adopt the practices in areas with the FHP. Vector control agents were responsible for breeding site control and instructed local residents on the Dengue Control Program. From 2001 to 2003, surveys were conducted to measure residents' dengue control knowledge and practices. The proportions of residents in the FHP area that reported health services as a source of information increased significantly as compared to the other area. There were significant changes concerning the increase in information about the disease and reduction in vector breeding sites. The results show that integration between the programs is possible and could help optimize resources, avoiding duplicity of procedures and fostering greater community involvement in dengue control.

Dengue virus surveillance: Detection of DENV-4 in the city of São José do Rio Preto, SP, Brazil.

Dengue viruses are the most common arbovirus infection worldwide and are caused by four distinct serotypes of the dengue virus (DENV). In the present study, we assessed DENV transmission in São José do Rio Preto (SJRP) from 2010 to 2014. We analyzed blood samples from febrile patients who were attended at health care centers in SJRP. DENV detection was performed using multiplex RT-PCR, using flavivirus generic primers, based on the genes of the non-structural protein (NS5), followed by nested-PCR assay with species-specific primers. We analyzed 1549 samples, of which 1389 were positive for NS1 by rapid test. One thousand and eight-seven samples (78%) were confirmed as positive by multiplex RT-PCR: DENV-4, 48.5% (528/1087); DENV-1, 41.5% (449/1087); DENV-2, 9.5% (104/1087); and co-infection (5 DENV-1/DENV-4, 1 DENV-1/DENV-2), 0.5% (6/1087). Phylogenetic analysis of the DENV-4 grouped the isolates identified in this study with the American genotype and the showed a relationship between isolates from SJRP and isolates from the northern region of South America. Taken together, our data shows the detection and emergence of new dengue genotype in a new region and reiterate the importance of surveillance programs to detect and trace the evolution of DENV.